In RepricerExpress, you can choose between using Channel Min/Maxs or Global Min/Max settings to set your Min/Maxs on Amazon.
At the moment you can only use the Global Min/Max option with eBay Repricing. This means that if you're currently using the Channel Min/Max setup for Amazon, you will be unable to add eBay as a channel.
If you would like to use eBay anyway there are a couple of things you can do. You can either contact support to have your account switched over to Global Min/Max or setup a separate RepricerExpress account for eBay repricing.